Human monoclonal antibodies that bind hepatitis C virus (HCV) E1

ABSTRACT

The present invention relates to materials and methods for treatment of hepatitis C. More closely, the invention relates to human monoclonal antibodies against HCV E1 antigen, to a reagent comprising such antibodies, and to vaccine compositions comprising such antibodies. Futhermore, the invention relates to a method of treating or preventing HCV infection by administration of a vaccine composition comprising the monoclonal antibodies of the invention.

This application is a §371 application of PCT/SE02/00044 filed 14 Jan. 2002, which in turn claims priority to US Provisional Application 60/260,889 filed 12 Jan. 2001. Each of the above identified applications is incorporated by reference herein.

FIELD OF THE INVENTION

The present invention relates to materials and methods for treatment of hepatitis C. More closely, the invention relates to human monoclonal antibodies against HCV E1 antigen, to a reagent comprising such antibodies, and to vaccine compositions comprising such antibodies for passive immunisation. Furthermore, the invention relates to a method of treating or preventing HCV infection by administration of a vaccine composition comprising the monoclonal antibodies of the invention for passive immunisation.

BACKGROUND OF THE INVENTION

Human monoclonal antibodies have been assumed as attractive agents for antagonist effects in many medical applications: anti-toxins, anti-receptor molecules, anti-cytokine reagents to reduce or abolish an inflammatory response, etc.

Hepatitis C virus (HCV) is a major global health problem, with at least 170 million people infected the world over. HCV results in a chronic infection in 75-80% of those initially infected (Houghton 1996). Very likely, immunological factors influence whether the infection will resolve spontaneously or become chronic. The latter will result in a liver inflammation of variable degree, an inflammation that after 10-20 years may result in cirrhosis (20% of chronic cases), and hepatocellular cancer (HCC; approx. 20% of those with cirrhosis) (Houghton 1996). Current pharmaceutical treatment will fail in 60% of the cases (alpha-interferon+Ribavirin). Thus, there is a need for improved therapy.

HCV was discovered in 1989. Scientific studies have been severely hampered by the fact that there is no robust method to propagate the virus in vitro. Thus, substances cannot be tested for the capacity to block infection by the virus (neutralization assay). Similarly, the only animal model available is chimpanzee, also limiting the number of studies possible (by cost, availability of animals. etc.). As a substitute for a neutralisation assay, the inhibition of binding of one of the two envelope proteins (E2) to target cells has been developed. This is called the NOB assay: neutralisation of binding. Recently, a replicon system where a subgenomic portion of the viral genome replicates inside cells (but is not assembled into viral particles) has been developed, and optimized.

As mentioned previously, the immune system may have an important role in determining the course of the infection. Both the cellular immune response, as well as the humoral immune system, have been implicated as important for the outcome of the HCV infection. The relative importance of them is still disputed.

Whether the humoral immune response (i.e. specific B-lymphocytes and antibodies) can interfere with the clinical course of the disease have gained increasing attention over the last years:

-   -   1. The kinetics of antibodies to the hypervariable region (HVR)         of E2 (one of the envelope glyco proteins) may be important:         early occurrence of anti-HVR antibodies correlate with         resolution of the acute infection.     -   2. Polyclonal anti-HCV immunoglobulin preparations given to         liver transplanted patients decreased the occurrence of         re-infection by HCV from 94% to 54%.     -   3. Polyclonal anti-HCV given to infected chimpanzees modulated         (ameliorated) the course of the infection.     -   4. Individuals lacking immunoglobulin have a tendency to get a         more severe and fast progressing disease compared to         immunocompetent individuals.     -   5. Anti-HCV antibodies (particularly NOB positive antibodies)         correlated with protection in vaccination experiments.

Accordingly, several groups and companies are currently exploring the possibilities of affecting the course of the infection by administration of anti-HCV antibodies, both to already infected and for prophylaxis (Burioni et al., 1998).

The present inventors have already cloned human antibodies to conserved regions of one of the two envelope proteins, E2 (Allander et al., 2000). These antibodies have NOB activity, and a patent application for them has been filed, i.e. WO 9740176. They bind to two or possibly three different regions (epitopes) on E2.

The role of E1 and E2 in the life cycle of the virus is not fully established, nor is the whole process of virus attachment and entry. Still, antibodies to the HVR of E2 can block infection in animals, and so can antibodies to other parts of HCV (most likely E2). Antibodies to E1 elicited by vaccination in chimpanzees correlated with reduced inflammation of the liver (despite constant viral levels in blood); the mechanism for this is unknown (Maertens et al., 2000). There is currently no report within prior art on human monoclonal antibodies to the E1 protein derived from combinatorial libraries.

SUMMARY OF THE INVENTION

The present inventors have been able to generate human antibodies to the E1 protein. This was much more complicated than isolating antibodies against the E2 protein, as there seem to be an immuno-dominance in most infected individuals to generate anti-E2 antibodies rather than anti-E1 inmunoglobulins. Initially, the inventors worked with a recombinant protein resembling the complexed E1/E2, the assumed native complex presented on the viral surface. Only anti-E2 antibodies could be isolated in those experiments. To solve the problem of generating anti-E1 antibodies, E1 was first cloned and expressed separately on the surface of eukaryotic cells. Subsequently, such E1 displaying cells were used for selection of anti-E1 binding clones from an antibody library displayed on filamentous phage, in order to avoid the immunodominant anti-E2 clones present in the phage antibody library.

In a first aspect, the invention provides a recombinant human monoclonal antibody, or antigen binding fragments thereof, that exhibits immunological binding affinity for a hepatitis C virus (HCV) E1 antigen, wherein said monoclonal antibody comprises an amino acid sequence homologous to the binding portion of a human antibody Fab molecule obtained from a combinatorial antibody library.

The monoclonal antibody according to the invention reacts with complexed HCV E1/E2 antigen. The monoclonal antibody according to the invention preferably reacts with genotypically different isolates of HCV virus. Furthermore, the monoclonal antibody according to the invention may be improved by mutation and new selection, i.e. so called affinity maturation in vitro, to increase the binding strength of the antibodies to E1.

The Fab molecule of the monoclonal antibody of the invention comprises the VH and VL domains respectively, of the heavy and light chains of the Fab molecule according to Seq. ID No. 1-56 of the enclosed Sequence Listning.

The monoclonal antibody according to the invention may be fused with a further substance for diagnostic or therapeutic purposes, for example a toxin, an antibody allowing targeting, e.g. against defense cells, a protein conferring modulated metabolism of the anti-E1 antibody, a marker for diagnosis, immunohistochemistry, imaging etc.

In a second aspect, the invention relates to a detecting immunological reagent comprising the monoclonal antibody according to the invention. For example, the reagent may be used in quantitative assays for detection and analysis of replication and assembly in the life cycle of the virus.

In a third aspect, the invention relates to an immunological assay comprising the above reagent. The assay may be a modified NOB assay as mentioned above. Alternatively, the immunoassay may be a qualitative assay to measure conformation of recombinant E1 in connection with the production of therapeutic and diagnostic agents.

In a fourth aspect, the invention relates to a drug or vaccine composition against HCV infection, comprising the monoclonal antibody according to the invention or any combination of antibodies, or antibody binding fragments, of the invention. The vaccine compositon is formulated with pharmaceutically acceptable vehicles in a conventional manner and is intended for passive immunisation.

According to the present invention it is possible to produce human antibodies to parts of E2 (in particular the HVR region), and to the envelope protein, E1, in order to compose a “cocktail” of 3-6 or more human monoclonal antibodies. Such a mixture of antibodies to different proteins and protein regions of the virus has a much larger probability of severely affecting such a variable virus as HCV.

In a fifth aspect, the invention provides a method of treating a subject against HCV infection in a therapeutic or prophylactic purpose, comprising administration of the vaccine composition according to the invention to subjects in need thereof.

DETAILED DESCRIPTION OF THE INVENTION Materials and Methods

Antibodies and Antisera

Monoclonal mouse anti-human-myc from Invitrogen was used in 1:1.50-1:75 dilution (9-19 μg/ml). Ascites produced mouse anti-E1 monoclonal antibody was diluted 1:250. A FITC conjugated rabbit-anti-mouse immunoglobulin from Dako was used as secondary antibody in 1:15-1:10 dilution (67-100 μg/ml).

Anti-HCV Phage Library Construction

The library was derived from a bone marrow donation from a patient infected with HCV genotype 1a. Construction of the library was performed as described in Allander et al., 2000. In brief, lymphocytes were isolated from bone marrow using Ficoll-Paque (Pharmacia), and total RNA was extracted by the acid guanidium thiocyanate-phenol method. First strand cDNA synthesis was performed using an oligo-dT primer and the “First strand cDNA synthesis” kit (Amersham Pharmacia). The cDNA was subsequently used as template for for PCR amplification of γ1 Fd and κ light chains (Kang et al., 1991), and ligated into the phagemid vector pComb3H (Barbas and Wagner, 1995).

Construction of E1 Expression Vector

The signal sequence and echtodomain of E1 (aa 174 to 359) was inserted into the vector pDisplay (Invitrogen). The pDisplay vector has a mouse Igκ signal sequence upstream of its cloning cassette and a PDGF membrane anchor sequence downstream of the cassette for cell-surface expression. In addition, the vector contains two tag sequences so that the expressed protein will have a N-terminal Hemagglutinin A epitope tag, and a C-terminal myc epitope tag before the membrane anchor. The signal sequence and echtodomain fragment of E1 was PCR amplified from a full-length HCV clone (pcv H77c, genotype 1a), which was a generous gift from Dr J Bucht, NIH, USA (Yanagi et al., 1997). Since the hemagglutinin A tag would be localized N-terminal of the E1 fragment and possibly disturb recognition by anti-E1 or anti-myc antibodies, the signal sequence and the Hemagglutinin tag were deleted from the vector using Eco RI and Pst I (Life Technologies). The E1 fragment was subsequently inserted with the 3′ end in the cloning cassette and the 5′ end replacing the removed sequences. The PCR was performed as follows: first 94° C. 5 min; then 94° C. 1 min, 52° C. 0.5 min, and 72° C. 10 min for 35 cycles; and f Primers (Symbion, Denmark) were designed to contain specific restriction enzyme sites for directional cloning and an ATG start codon in the sense primers: sense primer (H77C-S1b) 5′-GG AAC CTT CCT GAA TTC GGC TTG GGG ATG TTC TCT ATC-3′ (restriction site for Eco RI underlined), antisense primer (H77C-AS1) 5′-CAT GGA GAA ATA CGC CTG CAG CGC CAG-3′ (restriction site for Pst I underlined). The PCR fragment was cleaved with the mentioned restriction endonucleases, and gel purified on 1% agarose. The band of correct size (approx. 600 bp) was cut out from the gel, and DNA was eluted using Concert DNA purification kit (Life Technologies). The pDisplay vector (Invitrogen) was cut using the same restriction enzymes and likewise gel purified. The fragment was ligated to the vector in 1:1, 1:3 and 1:6 ratios at +4° C. o.n. using T4 DNA ligase (Life Technologies). The 1:1 ligation product was linearized, self-religated and used to transform E- coli (XL-1 Blue, Stratagene) by electroporation. Single ampicillin resistant clones were picked and cultured, and DNA was extracted using Wizard® Plus Midipreps DNA purification system (Promega). To distinguish which clones contained correct insert, DNA from single clones was analyzed both by PCR and by restriction enzyme digestion.

Detection of E1 Expression on Eukaryotic Cells

Expression of the E1-myc construct was tested in CHO and HeLa cells. Cells were grown in 6-well plates to near confluence in RMPI 1640 (CHO cells) or DMEM (HeLa cells) supplemented with 10% fetal bovine serum (FBS) and 100 U /ml penicillin, streptomycin 100 μg/ml (Life Technologies). Transfection was performed using FuGENE 6 (Boehringer-Mannheim) with a FuGENE 6 to DNA ratio of 3-6 μl to 1-2 μg per well. Geneticin (Life Technologies) was added to the culture media, in a final concentration of 200 μg/ml, 48 h after transfection. Analysis with immunofluorescence microscope (Leitz DMRBE, Leica) and flowcytometry (FacSort, Becton Dickinson) were carried out on solubilized cells. Cells were loosened using a rubber policeman and washed twice in wash buffer Dulbeccos' PBS, 0.5% FBS, 0.1% sodium azide (Life Technologies, USA). Cells were centrifuged and resuspended in a small volume of primary antibody (anti-myc or anti-E1) and incubated at RT for 60 min. After two to three washes in wash buffer, cells were incubated in the dark at RT for 30 min in secondary rabbit-anti-mouse Ig-FITC. Finally cells were briefly incubated in Hoerst 1:1000, washed 3 times and mounted on glass slides in 5-10 μl Vectashield(Vector). Cells to be analysed with flowcytometry were redisolved in 250 μl washbuffer.

Selection of Anti-E1 Clones

Anti-E1 clones were selected from three different sets of selections. For the first two sets, HeLa cells were grown to semi confluence in T75 culture flasks. In the first set of selections, cells were transfected with 8-9 μg E1 DNA (47-53 μl Fugene6). In the second set, HeLa cells were transfected twice with the E1 DNA to further increase the surface expression prior to selection. Cells were first transfected (5.5 μg DNA) in a T25 culture flask for two days, grown under Geneticin selection pressure for 5 days, and then moved and transfected in a T75 flask (16 μg DNA). In the third set, CHO cells were used because of their higher surface expression even after the first transfection. Cells were transfected with 16-30 μg DNA in T75 flasks. One to four days after transfection cells were harvested using a rubber policeman, and suspended in DPBS—4% nonfat milk—0.02% sodium azide. To deplete the phage library of non-specific binders, the phages were incubated with non-transfected cells for one hour on an orbit shaker 100 rpm at RT or incubated overnight at +4° C. and then on a turning-wheel (7 rpm) for one hour at RT. Cells were removed by centrifugation, and the depleted phages were incubated with transfected cells for 1.5-2 h on a turning-wheel at RT. Cells were then washed three times in wash-buffer (Dulbeccos PBS, 0.5% FBS, 0.02% sodium azide). Cells were resuspended in 100 μl anti-myc 1:75 dilution and incubated at RT for 2 h. After two washes the cells were resuspended in FITC-anti-mouse—IgG 1:15 dilution and incubated in the dark for 1 h. The cells were washed twice before resuspended (10⁶ cells/ml) in wash-buffer. Sorting was performed in a FACSVantage SE (Becton Dickinson). Phages were eluted from the sorted cells by adding 200 μl 0.1 M HCl-glycine pH 2.2. Eluted phages were used to infect freshly cultured XL-1 Blue. The infected bacteria were then plated out on LA-amp plates. The next day, colonies were harvested in SB and grown to a 50-100 ml culture. Phages were induced and harvested as described (Barbas et al., 1991), and used for a next round of selection.

Fab Expression and Initial Testing

Colonies were picked, propagated and analyzed as single clones. Fab production was induced and a periplasmic fraction was prepared by freeze thawing (Allander et al 2000). Fab production was determined in an ELISA using anti-Fd (The Binding Site, UK) and AP conjugated anti-Fab (PIERCE, USA). Specificity for the antigen was initially tested in an ELISA against an recombinant E1/E2 protein, or against recombinant E1 protein. The recombinant E1/E2 heterodimer protein (genotype 1a) expressed in CHO cells was generously provided by Dr M. Houghton, Chiron Corp. and has been described elsewhere (Spaete et al., 1992). The soluble E1 protein was expressed and secreted into the medium from COS cells, and was generously provided by Dr. A. Patel, MRC Virology Unit, Glasgow, U.K. The ELISA assays with these antigens were performed as described below.

ELISA Assay for Determination of Specific Binding of the Antibodies to HCV Proteins

ELISA for E1 reactivity: GNA lectin (Sigma) was diluted to 2.5 μg/ml in PBS and coated to microtiter wells (Costar 3690) over night at room temperature. The wells were washed once in PBS with 0.05% Tween 20 (PBS-T) and the wells were blocked with 4% non-fat dry milk in PBS for 2 hours at room temperature. A:fter discarding the blocking solution, 50 μl of recombinant E1 (approx. concentration 50 μg/ml) was added and incubated for two hours at room temperature. After the E1 solution had been discarded, the antibody preparations were added and bound antibodies detected as described below.

Recombinant E1/E2 heterodimer (genotype 1a) was diluted to 1 μg/ml in PBS, and coated to microtitre wells overnight at +4° C. Unbound antigen was discarded, and the wells were blocked with 5% non-fat dry milk in PBS for 60 minutes at room temperature. Blocking solution was discarded, and antibody solutions to be tested added in 1:3-1:24 dilutions (diluent: PBS with 0.05% Tween 20). The plates were incubated at 37° C. temperature for 2 hours, washed four times with PBS-T, and alkaline phosphatase (AP) coupled-goat anti-human F(ab′)₂ (Pierce, Rocherford, Ill.) antibodies in a 1:1000 dilution were added. After 60 minutes at 37° and subsequent washes, substrate solution (p-nitrophenyl phosphate, Sigma, St. Louis, Mo.) was added and absorbency measured at 405 nm.

For control purposes, recombinant E2 (genotype 1a), or BSA (Sigma) coated at 1 μg/ml were used in corresponding ELISAs to control for unspecific reactivity.

Transfer of Fab Clones into IgG Format

The Fd and the light chain gene segments were transferred from the phagernide vector pComb3H to the eukaryotic vector pcIgG1 as previously reported (Samuelsson et al., 1996). Plasmid DNA was transfected into CHO cells using Lipofectamine Plus (Life Technologies) according to the manufacturer's instructions. Medium containing secreted IgG was harvested every second day and frozen until analyzed. The ELISA to determine IgG concentration used a rabbit anti-human IgG and an AP conjugated rabbit anti-human IgG, and a purified human IgG standard as reference (Dako) (Samuelsson et al., 1996).

RESULTS

Library Size

Ligation of γ1 Fd genes into the pComb3H vector gave a library of 7.8×10⁶ cfu/μg, and ligation of κ light chain genes into the pComb3H gave a library of 1.6×10⁷ cfu/μg. The resulting combinatorial library comprised 3.7×10⁷ members.

Construction of E1 Expression Vector

The first ligation of pDisplay vector and E1 fragment resulted in similar number of clones independent of ligation ratios. Plasmid DNA extracted from cultures of the 1:1 ligation was linearized and separated on a gel. Two bands of approximately 5.5 and 6.0 appeared on the gel. Since the expected correct sized band was 5.8 kb, both bands were purified and religated separately. Single clones were grown and insertion of the fragment was demonstrated by PCR using the same sense and antisense primers as in the cloning step; 9 clones out of 20 showed the correct fragment length. Subsequent restriction enzyme digestion showed that the correct sized fragment also could be cleaved from all 9 clones. Nucleic acid sequencing of the clones showed that they all differed from the original E1 sequence by a few nucleotides or more.

Assessment of E1 Expression on Eucaryotic Cells

Initially HeLa cells were preferred. To determine optimal expression of the myc-tag, expression was investigated by fluorescence microscopy and flow cytometry on day 1, 2, 4, and 7 after transfection. This time study indicated that immunofluorescence detection of the myc tag was optimal 4 days after transfection. For the second set of selection surface expression was increased slightly by transfecting the HeLa cells twice. For the third set CHO cells were chosen since they appear to be more tolerant to transfection as well as show clear E1 expression already after one day of transfection.

Selection of E1 Specific Clones

In the first round of each selection series, approximately 10¹¹ cfiu of phage library was depleted against 10⁶-10⁷ non-transfected cells. Unbound, depleted phages were subsequently incubated with 3-8×10⁶ transfected, E1 expressing cells. After sorting for myc positive cells, phages were eluted from the sorted cells and re-propagated in fresh XL1 blue. 2-8×10¹⁰ cfu of re-propagated phages were used in the next selection round.

In the first series, two rounds of selection were performed. After the second round, only 108 colonies were formed, 98 of which were tested in ELISAs for Fab expression and binding to recombinant E1/E2 antigen. Sixteen clones expressed Fab, of which nine were positive for binding to E1/E2. After nucleic acid sequencing, two clones were judged not to be proper Fab fragments. Two clones (clones 13 and 98) from this selection series were further characterised and included in the present collection of antibodies (Table 1, Seq ID No. 1-4).

In the second series, six selection rounds were performed. After the fourth round, 42 single clones were picked and assayed for Fab expression. Twentytwo clones produced Fab, while only two were positive when tested for E1 reactivity. Subsequent sequence analysis revealed that the clones were identical (clone 4:6; Seq ID No. 13-14). An additional clone, isolated from the sixth panning round in this series, was also characterised (clone 6a:5; Table 1 and Seq ID No. 15-16).

In the third series, two rounds of selection were made and the second round was repeated once. 45-75% of propagated clones expressed Fab. The majority of our E1 specific Fab clones were isolated from this selection series (clones with prefix 1:, 2a: and 2b:).

Reactivity to HCV Antigens

The reactivity of the different Fab clones to the HCV proteins E1, E1/E2 in complex, free E2 or BSA was determined by ELISA. All clones showed a significantly higher reactivity to E1 and/or E1/E2 than against E2 or BSA (negative control antigens) (Table 1). From these data, it seems that some clones may be particularly efficient binders: clones 1.4, 1:8, 2a: 13, 2a:23, 2a:30, 2b:5 and 4:6

TABLE 1 Reactivity to HCV antigens and BSA by the Fab proteins (crude periplasmic preparations) as measured by ELISA (OD_(405 nm) values given). For technical reasons, E2 was in some experiments replaced with BSA as negative control antigen (values marked with (B)). n d = not determined μg Fab/ml Fab clone E1 E1/E2 E2 or BSA (B) (approximative) 13 0.20 0.16 0.03 (B) >3 98 0.20 0.16 0.10 (B) 5 1:4 0.78 0.67 0.27 (B) 0.01 1:8 0.75 0.53 0.09 (B) 0.01 1:9 0.96 0.67 0.16 (B) 0.05  1:10 0.20 0.12 0.01 (B) 0.01 4:6 0.97 0.20 0.08 0.24 6a:5  0.15 0.09 0.03 0.33 2a-2  1.00 0.32 0.18 0.64 2a-4  1.18 0.42 0.33 1.0 2a-5  0.89 0.08 0.07 0.44 2a-13 1.05 0.22 0.14 0.36 2a-14 0.36 0.09 0.07 0.72 2a-23 1.47 0.23 0.19 0.50 2a-25 1.46 0.33 0.24 0.11 2a-30 1.11 0.52 0.26 0.96 2a-32 0.61 0.09 0.07 >1 2a-33 0.65 0.14 0.14 >1 2a-37 0.99 0.48 0.29 (B) 0.08 2a-40 1.21 0.17 0.17 1.0 2b-1  0.35 0.12 0.08 0.94 2b-3  1.18 0.19 0.12 1.0 2b-4  0.11 0.09 0.03 (B) 0.68 2b-5  2.21 1.40 0.71 >1.0 2b-7  0.47 0.32 0.18 0.54 2b-9  0.33 0.19 0.15 0.19 2b-10 0.48 0.11 0.13 >1.0 2b-17 0.24 n d 0.05 0.16 mouse mcl anti-E1 >3.00 >3.00 0.20 rabbit anti-E2 n d 0.15 0.72 PBS 0.11 0.10 0.08 non-specific Fab 0.20 0.11 0.14 (B)

REFERENCES

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1. A recombinantly produced human monoclonal antibody or antigen binding fragments thereof having immunological binding affinity for hepatitis C virus (HCV) E1, wherein said monoclonal antibody or antigen binding fragment thereof comprises SEQ ID NO:
 49. 2. The monoclonal antibody or antigen binding fragment thereof according to claim 1, wherein the monoclonal antibody or antigen binding fragment thereof reacts with complexed HCV E1/E2 antigen.
 3. The monoclonal antibody or antigen binding fragment thereof according to claim 1, fused with a further substance for diagnostic or therapeutic purposes.
 4. An immunological reagent comprising the monoclonal antibody or antigen binding fragment thereof according to claim
 1. 